Abstract
Dickeya (formerly Erwinia chrysanthemi) species cause diseases on a wide range of crops and ornamental plants worldwide. Here we present the draft sequences of 17 Dickeya isolates spanning four Dickeya species, including five isolates that are currently unassigned to a species.
GENOME ANNOUNCEMENT
Species of the Dickeya genus (previously Erwinia chrysanthemi) of phytopathogenic bacteria cause disease in a wide range of plant species, including crops, worldwide (1). The Dickeya genus is currently described as having six species: dianthicola, dadantii, zeae, chrysanthemi, and paradisiaca (2, 3) and the newly described D. solani (4). Draft genome sequences of eight D. dianthicola and D. solani isolates were recently described (5), and four complete sequences of Dickeya strains, D. paradisiaca strain Ech703 (accession no. NC_012880), D. zeae strain Ech586 (accession no. NC_013592), D. chrysanthemi strain Ech1591 (accession no. NC_012912), and D. dadantii strain Ech3937 (accession no. NC_014500), along with a draft D. zeae strain sequence, have been deposited in GenBank.
We announce draft genome sequences of 17 isolates of Dickeya, including isolates of D. dadantii, D. chrysanthemi, D. zeae, and D. paradisiaca and five isolates currently unassigned to a species ( Table 1). The 12 isolates assigned to species are D. dadantii type strain NCPPB 898, isolated from pelargonium (Comoro Islands); former D. dadantii subspecies dieffenbachiae type strain NCPPB 2976, isolated from dieffenbachia (United States); D. dadantii NCPPB 3537, isolated from potato (Peru); D. chrysanthemi type strain NCPPB 402, isolated from chrysanthemum (United States); D. chrysanthemi biovar parthenii NCPPB 516, from Parthenium argentatum (Denmark); D. chrysanthemi NCPPB 3533, isolated from potato (United States); D. zeae CSL RW192, isolated from river water (England); D. zeae MK19, isolated from river water (Scotland); the D. zeae phylotype II type strain NCPPB 2538, isolated from maize (United States); D. zeae NCPPB 3531 and NCPPB 3532, both isolated from potato (Australia); and D. paradisiaca type strain NCPPB 2511, isolated from plantain (Colombia). The five isolates with unassigned species are CSL RW240/1 from river water (England), DW0440 from river water (Finland), MK7 from river water (Scotland), NCPPB 569 from sugarcane (Australia), and NCPPB 3274 from Aglaonema (St. Lucia).
TABLE 1.
Statistics for the 17 draft Dickeya genome sequences
| Species | Strain | Accession no. | No. of contigs | No. of assembled bases | N50 | No. of predicted coding sequences |
|---|---|---|---|---|---|---|
| D. chrysanthemi | NCPPB 402T | AOOA00000000 | 12 | 4,797,070 | 2,467,266 | 4,447 |
| D. chrysanthemi | NCPPB 516 | AOOC00000000 | 35 | 4,614,776 | 443,362 | 4,444 |
| D. chrysanthemi | NCPPB 3533 | AOOJ00000000 | 91 | 4,723,912 | 102,359 | 4,467 |
| D. dadantii | NCPPB 898T | AOOE00000000 | 52 | 4,933,637 | 191,282 | 4,591 |
| D. dadantii | NCPPB 2976T | AOOG00000000 | 84 | 4,810,532 | 114,781 | 4,552 |
| D. dadantii | NCPPB 3537 | AOOL00000000 | 47 | 4,805,222 | 222,170 | 4,430 |
| D. zeae | NCPPB 2538T | AOOF00000000 | 46 | 4,559,915 | 237,408 | 4,225 |
| D. zeae | NCPPB 3531 | AOOI00000000 | 29 | 4,623,158 | 385,197 | 4,256 |
| D. zeae | NCPPB 3532 | AONW00000000 | 19 | 4,555,162 | 330,312 | 4,261 |
| D. zeae | CSL RW192 | AONY00000000 | 56 | 4,696,643 | 240,868 | 4,402 |
| D. zeae | MK19 | AOOR00000000 | 35 | 4,669,100 | 417,168 | 4,346 |
| D. paradisiaca | NCPPB 2511T | AONV00000000 | 43 | 4,627,470 | 160,099 | 4,376 |
| Unassigned | NCPPB 569 | AOOD00000000 | 66 | 4,215,441 | 142,291 | 4,060 |
| Unassigned | NCPPB 3274 | AOOH00000000 | 62 | 5,110,316 | 166,211 | 4,729 |
| Unassigned | CSL RW240/1 | AONZ00000000 | 82 | 4,380,918 | 159,782 | 4,107 |
| Unassigned | DW0440 | AOON00000000 | 234 | 4,330,262 | 68,778 | 4,132 |
| Unassigned | MK7 | AOOO00000000 | 66 | 4,926,896 | 190,720 | 4,513 |
All strains were sequenced using 454 pyrosequencing (Roche, Branford, CT). Isolates NCPPB 402T and NCPPB 2511T were sequenced using paired-end libraries, and the remaining isolates were sequenced using single-end libraries. Sequences of nine strains (CSL RW192, CSLRW 240/1, DW0440, MK7, MK19, NCPPB 402T, NCPPB 2538T, NCPPB 2976T, and NCPPB 3531) were assembled de novo using 454 Life Sciences NEWBLER v2.5.3; meta-assemblies of NEWBLER de novo and reference-guided assemblies to the above-named sequences from GenBank were used for NCPPB 516 and NCPPB 3533 (to accession no. NC_012912); NCPPB 2511T (to accession no. NC_012880); NCPPB 569, NCPPB 898T, NCPPB 3274, and NCPPB 3537 (to accession no. NC_014500); and NCPPB 3532 (to accession no. NC_013592).
Coding sequences for each isolate were annotated using Prodigal and RAST gene callers and BLAST using query sequences known to be missed by those packages. tRNAScan-SE was used to identify tRNA sequences. A detailed comparative genomic analysis of these and previously published draft Dickeya sequences (5) will follow in a future publication.
Nucleotide sequence accession numbers.
The draft sequences of these Dickeya strains are available in GenBank under the following accession numbers: AONV00000000 (NCPPB 2511T), AONW00000000 (NCPPB 3532), AONY00000000 (CSL RW192), AONZ00000000 (CSL RW240), AOOA00000000 (NCPPB 402T), AOOC00000000 (NCPPB 516), AOOD00000000 (NCPPB 569), AOOE00000000 (NCPPB 898T), AOOF00000000 (NCPPB 2538T), AOOG00000000 (NCPPB 2976T), AOOH00000000 (NCPPB 3274), AOOI00000000 (NCPPB 3531), AOOJ00000000 (NCPPB 3533), AOOL00000000 (NCPPB 3537), AOON00000000 (DW0440), AOOO00000000 (MK7), and AOOR00000000 (MK19).
ACKNOWLEDGMENTS
This study was funded by the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS) (SCR/0919/07 and SCR/0927/09) and the Agriculture, Horticulture Development Board (AHDB) through the Potato Council (R437).
We thank members of the Centre for Genomics Research at the University of Liverpool for sequencing Dickeya strains used in the study.
Footnotes
Citation Pritchard L, Humphris S, Saddler GS, Elphinstone JG, Pirhonen M, Toth IK. 2013. Draft genome sequences of 17 isolates of the plant pathogenic bacterium Dickeya. Genome Announc. 1(6):e00978-13. doi:10.1128/genomeA.00978-13.
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